- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 21 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)
- 5 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)
SF4.2: 13 residues within 4Å:- Chain C: A.77, C.78, C.79, G.114, T.115, G.141, S.142, C.143, C.173, P.174
- Chain E: R.137, R.157, H.242
4 PLIP interactions:4 interactions with chain C,- Metal complexes: C:C.78, C:C.79, C:C.143, C:C.173
SF4.5: 11 residues within 4Å:- Chain F: C.173, I.174, H.175, C.176, T.177, R.178, C.179, C.223, P.224, V.225, A.227
4 PLIP interactions:4 interactions with chain F,- Metal complexes: F:C.173, F:C.176, F:C.179, F:C.223
SF4.6: 13 residues within 4Å:- Chain E: M.394
- Chain F: H.119, P.120, D.122, C.123, C.126, Q.128, G.129, C.132, L.134, Q.135, V.225, G.226
4 PLIP interactions:4 interactions with chain F,- Metal complexes: F:H.119, F:C.123, F:C.126, F:C.132
SF4.11: 12 residues within 4Å:- Chain H: H.111, C.133, P.134, I.138, C.162, I.163, Y.164, C.165, G.166, Y.167, C.168, E.179
5 PLIP interactions:5 interactions with chain H,- Salt bridges: H:E.179
- Metal complexes: H:C.133, H:C.162, H:C.165, H:C.168
SF4.12: 14 residues within 4Å:- Chain H: C.123, I.124, A.125, C.126, K.127, L.128, C.129, I.140, Y.155, C.172, P.173, V.174, A.176, I.177
4 PLIP interactions:4 interactions with chain H,- Metal complexes: H:C.123, H:C.126, H:C.129, H:C.172
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 21 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.10: 9 residues within 4Å:- Chain 3: E.100, E.104
- Chain B: N.8
- Chain G: E.10, Y.11, I.12, Y.14, W.15, V.19
Ligand excluded by PLIP3PE.13: 10 residues within 4Å:- Chain K: S.565, N.568, I.569, L.572
- Chain a: F.31
- Chain b: K.34, R.37, N.38, I.41, F.42
Ligand excluded by PLIP3PE.15: 17 residues within 4Å:- Chain K: N.159, K.162, S.163, L.165, S.166, L.169, G.228, L.229, L.235, N.559, I.562, L.563, G.566, L.567
- Chain L: K.429
- Chain a: P.83, D.84
Ligand excluded by PLIP3PE.18: 6 residues within 4Å:- Chain K: N.207, T.210, V.211, I.214, I.272
- Ligands: 3PE.21
Ligand excluded by PLIP3PE.19: 23 residues within 4Å:- Chain K: K.600, L.601, K.603, L.604, I.615, L.618, L.634, I.637, I.640, I.641
- Chain M: P.216, L.272, I.273, F.276, I.277
- Chain X: M.54, R.58, N.76, L.77, F.78, S.79, L.148
- Ligands: 3PE.24
Ligand excluded by PLIP3PE.20: 21 residues within 4Å:- Chain K: L.584, F.585, G.589, L.590, K.592, L.593, F.596, I.597, L.642
- Chain L: P.229, V.230
- Chain M: M.275, F.276, S.279, V.434, A.438, I.441
- Chain X: I.141, L.148
- Ligands: PLC.25, 3PE.56
Ligand excluded by PLIP3PE.21: 13 residues within 4Å:- Chain K: L.180, Y.184, N.207, M.208, V.211
- Chain L: I.411, S.414, L.415, L.421
- Ligands: 3PE.18
- Chain b: L.53, Y.57, F.63
Ligand excluded by PLIP3PE.22: 17 residues within 4Å:- Chain 5: L.158
- Chain K: F.7, I.61, M.62, W.74, F.76, F.122, V.126, V.138
- Chain L: L.461, I.465, I.466, Y.470, F.473
- Ligands: 3PE.23, PLC.52, PLC.53
Ligand excluded by PLIP3PE.23: 19 residues within 4Å:- Chain 5: E.206
- Chain 6: P.71, L.75, T.78, V.79, F.82, Q.83
- Chain 7: G.36, F.37, C.40, L.47
- Chain K: L.3, F.7, L.11, Y.59, N.60
- Ligands: 3PE.22, PLC.52, PLC.53
Ligand excluded by PLIP3PE.24: 24 residues within 4Å:- Chain 4: F.50, K.51, L.55, G.56
- Chain J: M.1, L.3
- Chain K: L.618, L.621, V.624, F.625, K.626, L.629, L.636
- Chain X: K.42, V.43, G.46, S.47, V.49, L.50, L.92
- Chain Z: Y.128, S.130, E.134
- Ligands: 3PE.19
Ligand excluded by PLIP3PE.27: 13 residues within 4Å:- Chain 2: A.3, A.6, G.7
- Chain L: Q.4, I.7, I.11, R.76, F.77, L.78, L.143
- Chain M: I.505
- Ligands: PLC.26, PLC.50
Ligand excluded by PLIP3PE.28: 14 residues within 4Å:- Chain 2: W.51, R.54
- Chain M: L.42, N.45, T.46, L.47, T.69, E.72, I.76, Y.491, V.492, S.495, L.496
- Ligands: PLC.49
Ligand excluded by PLIP3PE.30: 9 residues within 4Å:- Chain 0: M.41, M.42, P.45, R.48
- Chain G: Y.344
- Chain N: S.115, S.116, L.117
- Ligands: CDL.29
Ligand excluded by PLIP3PE.31: 7 residues within 4Å:- Chain 0: Y.9, Y.10
- Chain N: P.59, R.63, T.66, T.67
- Ligands: CDL.46
Ligand excluded by PLIP3PE.39: 10 residues within 4Å:- Chain X: F.102, L.105, Q.106, T.112, G.113, F.115, A.116, S.119, I.120, L.123
Ligand excluded by PLIP3PE.43: 11 residues within 4Å:- Chain 0: F.40, L.51, Y.52
- Chain G: I.342, F.346
- Chain Y: T.39, G.40, Y.44, S.47, L.48, R.51
Ligand excluded by PLIP3PE.47: 15 residues within 4Å:- Chain 0: L.17, S.18, A.21, H.22, F.28, Y.29, V.33
- Chain G: P.191, F.192, I.335
- Chain H: S.62, A.63
- Chain Y: F.32, C.36, T.39
Ligand excluded by PLIP3PE.51: 22 residues within 4Å:- Chain 4: L.4, F.7, A.10, V.11, F.14, R.18, Q.19
- Chain G: I.81, S.85, L.88, I.89, I.132, W.135
- Chain I: D.7, Y.14, E.23, A.26, I.27, A.30, M.33
- Chain O: Y.273, Y.274
Ligand excluded by PLIP3PE.54: 6 residues within 4Å:- Chain 8: Y.41, R.42, Q.45
- Chain K: F.468, Y.471
- Chain d: W.47
Ligand excluded by PLIP3PE.55: 7 residues within 4Å:- Chain K: F.585
- Chain X: S.136
- Ligands: 3PE.56
- Chain b: F.31, N.32, R.33, A.36
Ligand excluded by PLIP3PE.56: 12 residues within 4Å:- Chain K: L.584, F.585
- Chain X: S.137, A.140, I.141, V.143, G.144, S.147
- Ligands: 3PE.20, 3PE.55
- Chain b: K.30, F.31
Ligand excluded by PLIP- 5 x CDL: CARDIOLIPIN(Non-covalent)
CDL.29: 21 residues within 4Å:- Chain B: Y.98, I.101, I.102, L.105
- Chain I: L.141
- Chain M: F.3
- Chain N: K.13, F.14, S.15, R.19, S.115, S.116, L.117, F.140, P.141, W.142, F.143, V.145, A.146, N.147
- Ligands: 3PE.30
26 PLIP interactions:17 interactions with chain N, 6 interactions with chain B, 3 interactions with chain M- Hydrophobic interactions: N:F.14, N:F.14, N:F.14, N:F.140, N:W.142, N:W.142, N:W.142, N:F.143, N:V.145, N:V.145, B:Y.98, B:Y.98, B:I.101, B:I.102, B:L.105, B:L.105, M:F.3, M:F.3, M:F.3
- Hydrogen bonds: N:S.15, N:S.15, N:L.117, N:N.147, N:N.147, N:N.147
- Salt bridges: N:K.13
CDL.34: 9 residues within 4Å:- Chain B: Y.25, F.26
- Chain O: R.296, I.299, S.300, S.301, R.304
- Ligands: PLC.1, PLC.33
7 PLIP interactions:5 interactions with chain O, 2 interactions with chain B- Hydrogen bonds: O:S.301, O:R.304, B:Y.25, B:Y.25
- Salt bridges: O:R.296, O:R.304, O:R.304
CDL.42: 8 residues within 4Å:- Chain 1: L.26
- Chain H: Y.81
- Chain Y: R.24, G.25, F.26, R.27, I.30
- Ligands: PLC.41
9 PLIP interactions:1 interactions with chain 1, 7 interactions with chain Y, 1 interactions with chain H- Hydrophobic interactions: 1:L.26, Y:R.24, Y:I.30, H:Y.81
- Hydrogen bonds: Y:G.25, Y:R.27
- Salt bridges: Y:R.24, Y:R.24, Y:R.27
CDL.46: 18 residues within 4Å:- Chain 0: Y.6, Y.9, W.16, I.31, A.34, A.35
- Chain B: I.111, I.115
- Chain M: L.8, V.11, Y.12, L.15
- Chain N: S.60, R.63, I.64, T.67
- Ligands: 3PE.31, PLC.45
8 PLIP interactions:4 interactions with chain 0, 1 interactions with chain B, 2 interactions with chain M, 1 interactions with chain N- Hydrophobic interactions: 0:I.31, 0:A.34, 0:A.35, B:I.115, M:V.11
- Hydrogen bonds: 0:Y.9, M:L.15
- Salt bridges: N:R.63
CDL.48: 19 residues within 4Å:- Chain 1: G.15, S.16, W.20, I.23, R.24, L.27
- Chain H: Y.81, L.84, F.88
- Chain Z: M.1, I.2, F.4, L.7, I.8, A.11
- Chain f: X.1, S.4, I.5, Q.6
14 PLIP interactions:3 interactions with chain H, 3 interactions with chain 1, 6 interactions with chain Z, 2 interactions with chain f- Hydrophobic interactions: H:Y.81, H:L.84, H:F.88, 1:L.27, Z:I.2, Z:I.2, Z:I.8, Z:A.11, f:I.5
- Hydrogen bonds: 1:G.15, 1:S.16, Z:M.1, Z:I.2, f:S.4
- 1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NDP.32: 23 residues within 4Å:- Chain C: Y.204
- Chain O: G.46, T.48, G.49, F.50, L.51, R.71, F.93, I.95, L.114, I.115, G.116, F.124, V.129, V.152, S.153, S.154, Y.155, K.169, P.189, A.190, P.191, M.192
16 PLIP interactions:16 interactions with chain O- Hydrophobic interactions: O:Y.155
- Hydrogen bonds: O:G.46, O:T.48, O:T.48, O:G.49, O:F.50, O:L.51, O:L.114, O:G.116, O:G.116, O:K.169, O:M.192, O:M.192
- Salt bridges: O:R.71
- pi-Cation interactions: O:R.71, O:R.71
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)
EHZ.36: 19 residues within 4Å:- Chain S: S.86, L.87
- Chain V: R.21, V.24, L.25, Y.31, F.38, V.51, I.55, E.58, F.59, Q.62, R.63, V.65, K.71, L.74, A.78, Y.98, F.99
18 PLIP interactions:15 interactions with chain V, 3 interactions with chain S- Hydrophobic interactions: V:R.21, V:V.24, V:Y.31, V:F.38, V:V.51, V:I.55, V:E.58, V:F.59, V:Q.62, V:Y.98, V:F.99, S:L.87
- Hydrogen bonds: V:Q.62, V:R.63, V:R.63, S:S.86, S:S.86
- Salt bridges: V:R.21
EHZ.37: 23 residues within 4Å:- Chain K: Y.536
- Chain T: D.86, S.87
- Chain c: P.11, F.12, N.16, K.17, V.20, S.27, T.30, K.44, I.48, R.51, F.52, N.55, K.56, I.58, L.64, I.67, F.68, T.71, L.75, Y.78
15 PLIP interactions:13 interactions with chain c, 1 interactions with chain K, 1 interactions with chain T- Hydrophobic interactions: c:V.20, c:I.48, c:R.51, c:R.51, c:F.52, c:L.64, c:L.75, c:Y.78, K:Y.536
- Hydrogen bonds: c:F.12, c:N.16, c:N.55, c:N.55, c:K.56, T:S.87
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, C.S. et al., Global conformations of Pichia pastoris complex I are distinguished by the binding of a unique interdomain bridging subunit. Sci Adv (2025)


- Release Date
- 2025-10-15
- Peptides
- Altered inheritance of mitochondria protein 41, mitochondrial: A
NADH-ubiquinone oxidoreductase chain 3: B
BA75_00622T0: C
NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): D
NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): E
NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): F
NADH-ubiquinone oxidoreductase chain 1: G
NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): H
NADH-ubiquinone oxidoreductase chain 6: I
NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): J
NADH-ubiquinone oxidoreductase chain 5: K
NADH-ubiquinone oxidoreductase chain 4: L
NADH-ubiquinone oxidoreductase chain 2: M
NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): N
NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: P
NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): Q
NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): R
Acyl carrier protein: S
Acyl carrier protein: T
NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): U
BA75_04796T0: V
NADH-ubiquinone oxidoreductase: W
NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Z
NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 0
BA75_00589T0: 1
Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM: 2
BA75_05084T0: 3
NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 4
NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 5
NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 6
NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 7
Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 8
NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 9
NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): a
NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: d
NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit: f - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
1B
AC
BD
CE
DF
GG
HH
II
JJ
KK
LL
MM
NN
OO
PP
QQ
RR
SS
TT
UU
VV
WW
XX
YY
ZZ
a0
b1
c2
d3
e4
f5
g6
h7
i8
j9
ka
lb
mc
nd
oe
pf
q - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 21 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)
- 5 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 21 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
- 5 x CDL: CARDIOLIPIN(Non-covalent)
- 1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, C.S. et al., Global conformations of Pichia pastoris complex I are distinguished by the binding of a unique interdomain bridging subunit. Sci Adv (2025)


- Release Date
- 2025-10-15
- Peptides
- Altered inheritance of mitochondria protein 41, mitochondrial: A
NADH-ubiquinone oxidoreductase chain 3: B
BA75_00622T0: C
NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): D
NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): E
NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): F
NADH-ubiquinone oxidoreductase chain 1: G
NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): H
NADH-ubiquinone oxidoreductase chain 6: I
NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): J
NADH-ubiquinone oxidoreductase chain 5: K
NADH-ubiquinone oxidoreductase chain 4: L
NADH-ubiquinone oxidoreductase chain 2: M
NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): N
NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: P
NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): Q
NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): R
Acyl carrier protein: S
Acyl carrier protein: T
NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): U
BA75_04796T0: V
NADH-ubiquinone oxidoreductase: W
NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Z
NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 0
BA75_00589T0: 1
Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM: 2
BA75_05084T0: 3
NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 4
NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 5
NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 6
NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 7
Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 8
NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): 9
NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): a
NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: d
NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I): e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit: f - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
1B
AC
BD
CE
DF
GG
HH
II
JJ
KK
LL
MM
NN
OO
PP
QQ
RR
SS
TT
UU
VV
WW
XX
YY
ZZ
a0
b1
c2
d3
e4
f5
g6
h7
i8
j9
ka
lb
mc
nd
oe
pf
q - Membrane
-
We predict this structure to be a membrane protein.